D-I-TASSER Q8IXT5-D6

D-I-TASSER results for Q8IXT5-D6

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>Q8IXT5 (154 residues)
PPDEDFRGPPDEDFRHPPDEDFRSPQEEDFRCPSDEDFRQLPEEDLREAPEEDPRLPDNF
RPPGEDFRSPPDDFRSHRPFVNFGRPEGGKFDFGKHNMGSFPEGRFMPDPKINCGSGRVT
PIIVAMINYNEAMAAIKDLNDRPVGPRKVKLTLL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| PPDEDFRGPPDEDFRHPPDEDFRSPQEEDFRCPSDEDFRQLPEEDLREAPEEDPRLPDNFRPPGEDFRSPPDDFRSHRPFVNFGRPEGGKFDFGKHNMGSFPEGRFMPDPKINCGSGRVTPIIVAMINYNEAMAAIKDLNDRPVGPRKVKLTLL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCHHHHHHHCCCCCCCCCCSSSSSSC
Confidence	9530047897546689985346789621368998645578986677789976678897888986666789533578998556788998777889755567988776899777888885034798730466567876512578788622578749
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| PPDEDFRGPPDEDFRHPPDEDFRSPQEEDFRCPSDEDFRQLPEEDLREAPEEDPRLPDNFRPPGEDFRSPPDDFRSHRPFVNFGRPEGGKFDFGKHNMGSFPEGRFMPDPKINCGSGRVTPIIVAMINYNEAMAAIKDLNDRPVGPRKVKLTLL
Prediction	8477547544575474335753554457536543675365345754553457545447745436753544357446542575365455764744476345335653455463744443212010103424411320441774433444140326
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCHHHHHHHCCCCCCCCCCSSSSSSC
PPDEDFRGPPDEDFRHPPDEDFRSPQEEDFRCPSDEDFRQLPEEDLREAPEEDPRLPDNFRPPGEDFRSPPDDFRSHRPFVNFGRPEGGKFDFGKHNMGSFPEGRFMPDPKINCGSGRVTPIIVAMINYNEAMAAIKDLNDRPVGPRKVKLTLL

6zu9p

0.08

3.09

0.51

CEthreader

FPVIKSPYLKWPLVRWSYNDKYCARMVGDSLIVHDATKNFMPLEAKALKPSGIRDF--SFAPEGVKLQPFRNGDEPSVLLAYWTPETNNSACTATIAEVPRGRVLKTVTLHWQNQAEFLCFNVERHTKSGKTQFSNLQICRLTERDIPVEKVEL

5m27A

0.06

2.75

0.60

EigenThreader

YKKILVDDTDRMFPNSELMIQPIKSLLQTITQSHRVLEKYMPARVIYLINQGINPLTEKLPVNEVVILVNRYFSICTRIISAYGGEQGDAAIRTSLDIISELKQLRHHVEATNHLLYTGIGLSYGMGSSLKAVNVAARLEALTLPYALAFTAGV

2cqpA

0.34

0.16

4.66

0.47

FFAS-3D

--------------------------------------------------------------------------------MPFTVSIDEILDFF-YGYQVIPGSVCLKYNEKGMPTGEA---MVAFESRDEATAAVIDLNDRPIGSRKVKLVLG

6y5qq

0.10

3.62

0.92

SPARKS-K

ITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKDNQGNCYLKRESVELALKLLDEDEIRGKLHVEVAKFQLRVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKGQIRKLLLFDRHPDGVA--SVSFRDPEEADYCIQTLDGRWFGGRQITAQAW

4p6qA

0.26

0.06

1.81

0.62

CNFpred

-----------------------------------------------------------------------------------------------------------------------GMALVLYNEIEYAQAAVKETKGRKIGGNKIKVDFA

5mz61

0.07

0.06

2.45

0.83

DEthreader

-IEKDELNCTGFEQTAQQSELFIFISLSKLARTSYYASFLRVALVTTTLAYYSSMRCVYMAISD-FSQLSIKHFNDEFARIRERGMSSQVLMH---RDS-S---VR-PR--P-NII-NEIGMCVWLDDTMEIFNNALKIVRYL------MIAVL

1e9iD2

0.10

3.60

0.82

MapAlign

KAKGMNTAVGDEGGYAPNLGSNAEALAVIAEAVKAAGYELGKDITLAMDCAASEFYKDGKYVLAGENKAFTSEEFTHFLEELTKQYPIVSIEDKIQLVGDDLFVTNTKILKEGIEKGIANSILIKIGSLTETLAAIKMAK-----DAGYTAVIS

6nn3A1

0.10

0.09

3.36

0.67

MUSTER

-CSQHFYEMYNPLYGSRLGVPDTLGGDPKFRSLTHEDHAIQPQNFMPGPLVNSVSTLTGLSTGTSQNTRIS--LRPGPVSQPYHHWDTDKYVTGINAISHGQGVGRFPNEKEQLKQLQGLNMHTYFPNTDQIERPLM-WNRRA-----------

5uz5F

0.21

0.12

3.72

0.73

HHsearch

-----------------------NH-MSQFIYPVQQQP-----------SLN------HFTDPNNTFIVTEDELRAY--FQ----------PFG-----TIVYVKIPVG-------KC--CGFVQYVDRLSAEAAIAGMQGFPIANSRVRLSWG

1e1cA

0.09

3.45

0.49

CEthreader

GTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAASVAFDLPTHRGYDSGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQ

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5139

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1uarA	0.45	4.71	0.051	0.714	model1_1uarA.pdb.gz
2	1qi9A	0.45	5.16	0.043	0.805	model1_1qi9A.pdb.gz
3	3bxwB	0.45	4.72	0.038	0.753	model1_3bxwB.pdb.gz
4	3iiiA	0.44	5.48	0.041	0.825	model1_3iiiA.pdb.gz
5	2eg4A	0.41	4.69	0.048	0.682	model1_2eg4A.pdb.gz
6	3hzuA	0.41	4.89	0.040	0.701	model1_3hzuA.pdb.gz
7	4s3jA	0.40	5.02	0.027	0.688	model1_4s3jA.pdb.gz
8	4q6tA	0.37	5.79	0.038	0.714	model1_4q6tA.pdb.gz
9	1yt8A	0.37	5.05	0.052	0.610	model1_1yt8A.pdb.gz
10	1itxA	0.35	5.15	0.014	0.649	model1_1itxA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:1901363	0.97	heterocyclic compound binding
GO:0097159	0.97	organic cyclic compound binding
GO:0044822	0.95	poly(A) RNA binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.90	single-organism process
GO:0009987	0.85	cellular process
GO:0048856	0.83	anatomical structure development
GO:0044767	0.80	single-organism developmental process
GO:0065007	0.73	biological regulation
GO:0050789	0.72	regulation of biological process
GO:0044763	0.71	single-organism cellular process
GO:0050794	0.70	regulation of cellular process
GO:0048518	0.64	positive regulation of biological process
GO:0051179	0.63	localization
GO:0007165	0.63	signal transduction
GO:0048522	0.61	positive regulation of cellular process
GO:0016043	0.59	cellular component organization
GO:0080090	0.58	regulation of primary metabolic process
GO:0048869	0.58	cellular developmental process
GO:0048519	0.58	negative regulation of biological process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0008104	0.58	protein localization
GO:1902578	0.57	single-organism localization
GO:0051128	0.57	regulation of cellular component organization
GO:0048583	0.57	regulation of response to stimulus
GO:0048468	0.57	cell development
GO:0031325	0.57	positive regulation of cellular metabolic process
GO:0022607	0.57	cellular component assembly
GO:0051130	0.56	positive regulation of cellular component organization
GO:0048585	0.56	negative regulation of response to stimulus
GO:0048523	0.56	negative regulation of cellular process
GO:0045937	0.56	positive regulation of phosphate metabolic process
GO:0043085	0.56	positive regulation of catalytic activity
GO:0002064	0.56	epithelial cell development
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0051050	0.55	positive regulation of transport
GO:0008285	0.55	negative regulation of cell proliferation
GO:0051641	0.54	cellular localization
GO:0044802	0.54	single-organism membrane organization
GO:0023051	0.54	regulation of signaling
GO:0022402	0.54	cell cycle process
GO:0010646	0.54	regulation of cell communication
GO:0010604	0.54	positive regulation of macromolecule metabolic process
GO:0072015	0.53	glomerular visceral epithelial cell development
GO:0071850	0.53	mitotic cell cycle arrest
GO:0060395	0.53	SMAD protein signal transduction
GO:0051898	0.53	negative regulation of protein kinase B signaling
GO:0051291	0.53	protein heterooligomerization
GO:0043113	0.53	receptor clustering
GO:0032926	0.53	negative regulation of activin receptor signaling pathway
GO:0032516	0.53	positive regulation of phosphoprotein phosphatase activity
GO:0030336	0.53	negative regulation of cell migration
GO:0002092	0.53	positive regulation of receptor internalization

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.86	cytoplasmic part
GO:0043226	0.84	organelle
GO:0043229	0.83	intracellular organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0005737	0.73	cytoplasm
GO:0005634	0.73	nucleus
GO:0016020	0.70	membrane
GO:0005886	0.61	plasma membrane
GO:0045202	0.58	synapse
GO:0043232	0.58	intracellular non-membrane-bounded organelle
GO:0097458	0.56	neuron part
GO:0048471	0.55	perinuclear region of cytoplasm
GO:0030054	0.55	cell junction
GO:0036057	0.51	slit diaphragm
GO:0014069	0.51	postsynaptic density
GO:0005923	0.51	bicellular tight junction
GO:0044422	0.50	organelle part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2e5dB	0.422	5.01	0.049	0.740	2.4.2.12	NA
2	0.060	1iq8A	0.407	5.25	0.047	0.753	2.4.2.29	29
3	0.060	1yr2A	0.405	4.51	0.035	0.617	3.4.21.26	45
4	0.060	3a2pA	0.415	4.80	0.049	0.708	3.5.2.12	NA
5	0.060	1okgA	0.384	5.46	0.056	0.727	2.8.1.2	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	1v0fC	0.332	5.50	0.076	0.636	0.59	SIA	complex1.pdb.gz	90,91,93,95
2	0.01	3gvlA	0.432	5.16	0.059	0.766	0.47	SLB	complex2.pdb.gz	78,89,103
3	0.01	3gvjA	0.421	5.34	0.072	0.786	0.51	UUU	complex3.pdb.gz	78,89,103
4	0.01	1v0fE	0.332	5.33	0.033	0.623	0.61	SIA	complex4.pdb.gz	91,92,94,96,98
5	0.01	3gvkB	0.326	5.44	0.017	0.617	0.47	UUU	complex5.pdb.gz	80,91,93,94,95

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.